I installed the iOS 7 GM yesterday from iOS 6. I noticed the iMessages on my phone and on my MacBook Pro don't sync at all. For example, if I have a conversation on iMessage via my MBP, NONE of the conversation shows up on my phone. And vice versa.
Make sure in the message setting you have send and receive checked for both your phone number and your email address. Sometimes after restoring, one of the devices is only sending/receiving from email address or vise versa. That may not be it, but I have had that happen before.